compareGenotypes {beadarraySNP} | R Documentation

## Compare genotypes

### Description

Pairwise comparison of genotypes between unaffected and affected tissue from the same subject

### Usage

    compareGenotypes(genotypeT, genotypeN)

### Arguments

`genotypeT` | character or logical vector, genotypes of affected tissue
`genotypeN` | character or logical vector with same length as genotypeT, genotypes of unaffected, normal tissue

### Details

Heterozygous probes have one the following values. `TRUE`, `'H'` or `'AB'`. All other values are considered homozygous. The primary purpose of the method is to find probes with loss of heterozygosity (LOH), where the unaffected probe is heterozygous and the affected is called homozygous.

### Value

A vector with the same length as the arguments where each element can have one of four values

`'u'` | Uninformative: both affected and normal are homozygous
`'i'` | Informative: both affected and unaffected heterozygous
`'l'` | Loss: unaffected heterozygous, affected homozygous
`'a'` | Artefact: unaffected homozygous, affected heterozygous

### Author(s)

Jan Oosting

### See Also

`heterozygousSNPs`

### Examples

    data(chr17.260)
    compareGenotypes(exprs(chr17.260)[,"514TV"],exprs(chr17.260)[,"514NP"])

[Package beadarraySNP version 1.60.0 Index]